Gromit - I had this problem when working on the textures for the PocketWatch. I had groups that where layered through the model such as the front and back caps and the front and back faces. I brought the mesh into 'Mapper then set it up so I was looking through the layers. For each set of groups I wanted, I'd select everything else and scale them very small then move them into a corner of the template. I then repeated the process using the same mapping each time till I had several templates, one for each layer. After making the textures, I applied each on to the approperiate layer in Poser. Just make certain you've de-selected 'apply to entire figure' when you apply them. This, of course, doesn't work for all problems of this type but it does help in many instances.